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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
Published on: October 27, 2017
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Erik Kristiansson1, Noomi Asker, Lars Förlin
1Department of Zoology, University of Gothenburg, Göteborg, Sweden. erik.kristiansson@zool.gu.se
BMC Genomics
|August 4, 2009
Summary
This study characterizes the Zoarces viviparus liver transcriptome, identifying over 50,000 transcripts. This genomic data enables the development of gene expression microarrays for marine ecology research.
Area of Science:
- Marine Biology
- Genomics
- Environmental Monitoring
Background:
- Zoarces viviparus (eelpout) is a key marine model organism.
- Limited genomic data has hindered molecular studies of this species.
- Previous research lacked comprehensive gene expression analysis tools.
Purpose of the Study:
- To perform the first comprehensive characterization of the Zoarces viviparus liver transcriptome.
- To generate sequence data for designing gene expression microarrays.
- To facilitate genome-wide research in Zoarces viviparus.
Main Methods:
- Massively parallel pyrosequencing (454 Life Science/Roche Genome Sequencer FLX).
- De novo assembly, annotation, and functional classification of transcripts.
- Design of an oligonucleotide microarray based on generated sequence data.
Main Results:
- Over 50,000 putative transcripts assembled and annotated from 400,000 reads.
- Transcriptome data covers approximately 40% of the total transcriptome.
- Homologues for about half of the genes in Gasterosteus aculeatus identified.
Conclusions:
- A single sequencing run provides sufficient genomic information for higher vertebrate transcriptome assembly.
- The generated sequence data and microarray probes are publicly available.
- This resource will advance molecular-level environmental monitoring and marine ecology research.
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